jmol-developers

Bugs item #1688735, was opened at 2007-03-26 15:46
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Category: Graphics
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Miguel (migueljmol)
Summary: mo's of a single atom
Initial Comment:
Hi,
My real plan at one point in time is to have Jmol show some fake hybrid orbitals for single atoms. (This is why I wrote earlier about the cube file and jvxl file problems/bugs I found).
Now I decided that I should be able to do this by modifying coefficients in a Spartan.spartan file and pretend that Spartan calculated the hybrids (this is how I did it earlier: modify coefficients, calculate surfaces and do screen captures). Then I would like to use the mo xx command to have Jmol show the hybrid orbitals.
To my surprise, I don't see any orbital when I do that for a single atom structure. If I calculate H2O, it works, but not a single atom.
Jmol knows that there are 9 orbitals in the file (since if I ask for mo 12, it tells me an index from 1 to 9 is required). I tried it with C and that worked (for mo's 1-4 of course), but not Fe.
Any idea why?
Just in case, I'll attach the Fe.spartan file.
----------------------------------------------------------------------
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1688735&group_id=23629

Bugs item #1688735, was opened at 2007-03-26 15:46
Message generated for change (Comment added) made by rkanters
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1688735&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Graphics
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Miguel (migueljmol)
Summary: mo's of a single atom
Initial Comment:
Hi,
My real plan at one point in time is to have Jmol show some fake hybrid orbitals for single atoms. (This is why I wrote earlier about the cube file and jvxl file problems/bugs I found).
Now I decided that I should be able to do this by modifying coefficients in a Spartan.spartan file and pretend that Spartan calculated the hybrids (this is how I did it earlier: modify coefficients, calculate surfaces and do screen captures). Then I would like to use the mo xx command to have Jmol show the hybrid orbitals.
To my surprise, I don't see any orbital when I do that for a single atom structure. If I calculate H2O, it works, but not a single atom.
Jmol knows that there are 9 orbitals in the file (since if I ask for mo 12, it tells me an index from 1 to 9 is required). I tried it with C and that worked (for mo's 1-4 of course), but not Fe.
Any idea why?
Just in case, I'll attach the Fe.spartan file.
----------------------------------------------------------------------
>Comment By: Rene Kanters (rkanters)
Date: 2007-03-26 15:48
Message:
Logged In: YES
user_id=905185
Originator: YES
File Added: C.spartan
----------------------------------------------------------------------
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https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1688735&group_id=23629

Bugs item #1688735, was opened at 2007-03-26 15:46
Message generated for change (Comment added) made by hansonr
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1688735&group_id=23629
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Graphics
Group: None
>Status: Closed
>Resolution: Later
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Miguel (migueljmol)
Summary: mo's of a single atom
Initial Comment:
Hi,
My real plan at one point in time is to have Jmol show some fake hybrid orbitals for single atoms. (This is why I wrote earlier about the cube file and jvxl file problems/bugs I found).
Now I decided that I should be able to do this by modifying coefficients in a Spartan.spartan file and pretend that Spartan calculated the hybrids (this is how I did it earlier: modify coefficients, calculate surfaces and do screen captures). Then I would like to use the mo xx command to have Jmol show the hybrid orbitals.
To my surprise, I don't see any orbital when I do that for a single atom structure. If I calculate H2O, it works, but not a single atom.
Jmol knows that there are 9 orbitals in the file (since if I ask for mo 12, it tells me an index from 1 to 9 is required). I tried it with C and that worked (for mo's 1-4 of course), but not Fe.
Any idea why?
Just in case, I'll attach the Fe.spartan file.
----------------------------------------------------------------------
>Comment By: Bob Hanson (hansonr)
Date: 2007-06-03 13:47
Message:
Logged In: YES
user_id=1082841
Originator: NO
Jmol cannot display MOs for calculations using a 5D basis set. (Standard
is 6D.) However, the Spartan smol reader was not indicating that the set
was 5D, so an exception was being thrown when it came time to do the
calculation. (There were too few coefficients.) If you look on your Java
console, you will see "Error in MO Calculation" displayed.
I have made changes to 11.1.47 to handle this better; the Java Console
will now read in this case:
QuantumCalculation.checkCalculationType: can't read 5D basis sets yet:
PM3D 1 5D shells -- exit
At some future date, Jmol might be able to read a 5D basis, but for now,
if it is at all possible, try a different basis for the calculation.
Bob
----------------------------------------------------------------------
Comment By: Rene Kanters (rkanters)
Date: 2007-03-26 15:48
Message:
Logged In: YES
user_id=905185
Originator: YES
File Added: C.spartan
----------------------------------------------------------------------
You can respond by visiting:
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